Equestria Eclipsed
by MadManMatt64
Summary: After the disappearance of the ponies of Trottingham, the Mane 6 go to investigate, along with Princess Celestia, who has taken a personal interest in the case. After investigating, it is revealed that what happened has ties to the origins of Equestria, and the princesses. Along the way, friendships are tested, and a villain as old as Equestria reveals himself...
1. Prologue

Equestria Eclipsed

Prologue- A Quiet Day

It was a quiet day in Trottingham. That in and of itself was a bit of an odd thing. Normally, the small town was full of all kinds of life. Normally, there were foals playing in the streets, and ponies bartering for goods in the marketplace, and the chatter of friends in the local hotspots. Yet, that wasn't the case for today. And the moment that a stallion named Dust Cloud had arrived back in town, it felt... strange. Like someone had pressed the mute button on the entire world.

Dust cautiously walked town the streets of the town, casting glances this way and that. He felt a deep pit in his stomach that wouldn't go away, and a small panic started to wash over him. "I-It can't be...", he thought to himself as he continued to walk around town, and look into buildings, and peek around every corner. And as he looked, a realization slowly dawned on him. One that made him go wide-eyed with fear.

Everypony was gone.

When Dust Cloud realized this, his panic started to grow. He had only been here this morning, and when he was there, Trottingham was just like how it always was. He would've sworn he left the town only thirty minutes ago just to go and look around the outskirts of the nearby forest to find flowers for his marefriend! And so, without any other options, he ran back home, crying for his marefriend. But when he reached his home and opened the door, a sinking sensation filled his entire body as he realized that even his lover was gone. It was at this moment the horrible reality began to sink in, and he walked out of his house, tears in his eyes, and the feelings of both sadness and fear welling inside him. And then, out of nowhere, he heard a voice say, "Well, it looks as though we've found a straggler, haven't we Chain?"

The young colt suddenly looked up at the new voice and asked meekly, "Wh-Who's there...?"

A second voice joined in, ignoring Dust's inquiry, "An earth pony by the looks of it, Ball. Hmph. I'm surprised that the brute was able to evade us for so long..."

"Who're you callin' a brute!", Dust shouted, indignant.

The two ponies laughed, and it sent chills down the young stallion's spine. He couldn't find them, no matter where he looked, and their voices seemed to be coming from all directions. Finally fed up with all of this, Dust decided to make a break for the forest, and ran in the direction that he came in. And he didn't stop running... at least, until he bumped into another pony and fell back. Looking up, Dust saw two hooded ponies. Their eyes weren't seen, but the first thing he noticed, aside from their evil grins, were their horns, both glowing with yellow magic.

"Well Chain, I believe it's your turn.", said Ball.

"It is indeed.", replied Chain, "It's time to meet your new masters..."

And then, there was a scream... and it was a quiet day in Trottingham once again.


	2. An Abandoned Town

"Mutual caring relationships require kindness and patience, tolerance, optimism, joy in others achievements, confidence in oneself, and the ability to give without undue thought of gain."

-Fred Rogers

Chapter 1- The Abandoned Town

Twilight's castle gleamed brightly in the morning sun, it's light reflecting off the crystal and making the ground around it glisten in vibrant light and dark purple hues. It had been only a week after Tirek attempted to take all the magic out of Equestria, but you wouldn't know by the way Ponyville looked. Everypony there was as bright and as cheerful as ever, and the new castle served as a reminder that as long as Princess Twilight Sparkle was there to watch over them all, they would never be in danger. So, what was the Princess doing? Reading up on the political history of other nations? Attempting to solve the problems of all the ponies in her care? Spending minute after painstaking minute researching some new experimental magic?

Well... not exactly.

"Helllooooooooo!", Pinkie Pie called out, before sticking out her ear, and listening to her echoing voice call back to her. She giggled a little and said, "This is fun! Twilight, you gotta try this!"

Twilight chuckled as she motioned Pinkie Pie to follow her and the rest of the group to the throne room to talk. Pinkie complied and bounded up the group, however still keeping her attention on the vaulted ceiling. After a moment, Twilight said, "It's great finally being able to see you all again, girls!"

"It's good to see you too, darling.", Rarity said, smile on her face, "I can hardly believe it took us this long to all come over."

"Well, what do you expect?", Rainbow Dash asked, "I mean, after that whole Tirek thing, Equestria was totally out of whack. It took the Weather Team days before we were able to get the weather back on schedule."

"And it took quite some time for all my animals to calm down...", Fluttershy added meekly.

"Not ta mention the fact that all the farms were failin' without anyone ta tend 'em.", Applejack said, "Ah'm surprised that we were even able to save most of the apple trees."

"And all my balloons and streamers were gone!", Pinkie Pie shouted, "How does that even happen!?"

Twilight smiled, "Well, regardless of all that, I'm glad that we're finally able to put all of that behind us, and just talk."

Fluttershy then noticed something, "Um, Twilight... where's Spike?"

"Oh, he wanted to make some cookies for us. He'll probably be done with them soon.", Twilight explained as she used her magic to open the throne room doors.

"Oh, I see.", Fluttershy said, knowing how much the dragon loved making sweets.

Just as they were about to enter the throne room, the door to the castle burst open, and a guard pony came barreling in, out of breath. Twilight immediately sensed that something was wrong, and took flight, flapping over to the pony as fast as her wings could take her, attempting to meet him half-way. However, before he could even get to half-way, his legs gave out, and he collapsed onto the floor. Twilight glided down to the downed guard, and landed next to him. He was panting heavily, no doubt having run a great distance. Realizing that the pony was probably dehydrated after running for so long, Twilight conjured a glass of water and magically held it to the pony's lips. He gulped the water greedily, and once he got to the bottom of the glass, breathed out a huge sigh of relief and continued to breathe heavily, but he no longer panted. Twilight then asked him, "Are you okay? What's wrong?"

The guard looked at Twilight in the eyes and said, "P-Princess Twilight... it's... Trottingham."

Twilight looked at the pony intently, not realizing that all of her friends had gathered around her and the fatigued guard. However, the guard only had eyes for Twilight, and he continued on with, "Trottingham... it's... abandoned..."

This made Twilight and the others' eyebrows raise. After all, Trottingham was a pretty close facsimile to Ponyville, the only major difference being it's bigger unicorn population. It was by no means a bustling city, but it was certainly big enough that it would just be abandoned. She then asked, "Are you sure?"

The guard nodded, some of his strength returning, and said, "There was... nopony there. And everything... looked untouched... like they all just left..."

The more and more Twilight listened, the less and less she believed that something like this could happen. And yet... there was no denying the fact that the look in the poor stallion's eyes was that of a pony who spoke the absolute truth. She had spent enough time with Applejack to know that look inside and out. She was about to say something to the guard, but he abruptly tried to sit up, saying, "Must.. warn Princess Celestia..."

Surprisingly, Rainbow Dash was the one to calm him down, saying, "Whoa there big guy. You did enough already. You really deserve a break after running...", she turned to Twilight and asked, "What's the distance from here to Trottingham?"

"About 50 or so miles.", Twilight said, "The only reason he's probably still alive is because he's an earth pony..."

"Dang, 50 miles!?", Rainbow said, "Alright, that's it. You need rest."

"But... I must warn...", he said as he stood up on shaky legs, attempting to protest.

At this point, Twilight stepped in again, saying, "Don't worry we'll deliver the message to Princess Celestia. You've earned a rest."

"...Thank you.", was all the guard said, before collapsing onto the ground again and snoring loudly.

An awkward silence fell around the group, and they all looked at each other, wordlessly expressing their confusion over what had just transpired. After a few moments, the pony that first spoke was Rarity, who said, "Well... I suppose that means we're going to Canterlot then."

"Yes, but we should really put him in a bed. Laying down on the floor can't be good for him.", Fluttershy pointed out.

Twilight nodded and was about to as a guard to carry the messenger to one of the guest rooms, when a voice called out, "Hey everypony! I got some nice cookies, fresh outta the-"

The whole group turned to look at the source of the voice, and it turned out that it was Spike, rolling a trolly filled with cookies. He had a look of exasperation on his face as he said, "Okay, what's happening in what part of Equestria now?"

"What do you mean, Spike?", Twilight questioned.

"I mean you've got a guard pony laying down face first in the carpet. If something big _wasn't_ going on, I would be surprised.", He said, folding his arms.

Rarity then said, "Oh, Spike, it's hardly like the fate of Equestria hangs in the balance or anything of the sort. It's just that a lot of people have gone missing is all."

"And that doesn't sound like something big?", Spike asked.

It was then that Applejack spoke up, "Well, honestly Spike, this ain't exactly the most dangerous thing we've come across. Ah mean, we've fought Nightmare Moon, Discord, Chrysalis, Sombra, and Tirek, and we've beaten all kinds a creatures and all kinds a bad ponies. Ah think we can handle a few missing townspeople."

Spike looked unsure for a moment, before sighing and saying, "Yeah, you're right. I guess one town going missing isn't the biggest thing to happen in Equestria."

"And if there are any mean ponies or critters responsible, we'll send 'em packing like always!", Pinkie said gleefully.

"Oh goodness, I don't know any creature that can make ponies disappear...", Fluttershy said, before continuing, "But if it is an animal, I'll be sure to give it a really stern talking to."

"Yeah, that's right!", Rainbow said, voice brimming with confidence, "We'll be able to take on anything that comes our way, cuz when we're all together, nopony, and I mean nopony can stop us!"

Twilight smiled to herself. They all really had grown as friends and as individuals ever since she had come to Ponyville, and she agreed with Rainbow Dash wholeheartedly. She now couldn't ever imagine a life outside of Ponyville, and she was now here to stay by the sides of her friends.

It was in the middle of all these warm and fuzzy feelings that she suddenly remembered what it is that she was going to do in the first place. She called over a unicorn guard, and ordered him to take the winded pony to one of the guest rooms. He wordlessly complied and lifted the pony up with his and carried him off. She then said, "Spike, could you please take a letter to Princess Celestia?"

Spike looked at Twilight oddly before saying, "Wow, really? Boy, I haven't done that for a while... but, uhh, sure! I just gotta find a quill, ink, and parchment is all."

Without a word, Twilight conjured up all the supplies that Spike would need, and set them down beside him. He said, "Thanks.", before holding up the paper and asking, "Alright, what's the message?"

Without wasting time, Twilight began, "Dear Princess Celestia. I know that I haven't sent you one of these letters for a while, but I have to tell you something that happened. A few minutes ago, a guard pony came rushing into my castle, claiming that Trottingham's population had mysteriously disappeared. I told him that I would warn you of what has happened, and I await your response. Your Faithful Student, Twilight Sparkle. Did you get all that Spike?"

"Yep, every single word.", Spike said, rolling it up and blowing flame onto the piece of parchment so that it would be sent to Celestia.

After a few moments of nothing, Rainbow Dash spoke up, saying, "Umm... how long is this gonna take?"

"I don't know.", Twilight said, "It could take hours. I mean, Princess Celestia has been really busy ever since Tirek escaped. She probably won't get the message until-"

She was interrupted when Spike burped up a letter, not thirty seconds after sending the last one.

As Twilight picked up the letter, the whole group was silent. Even Pinkie Pie was being uncharacteristically quiet. Then, Twilight unrolled the letter, and read it aloud, "Dear Princess Twilight. This is most alarming news, and I thank you for telling me this as soon as you heard it. I will be going to Trottingham to investigate the disappearances, and I would very much appreciate it if you and your friends would accompany me. I have my suspicions on what might have happened, but I won't say what they are until I know for sure. Please, be there as soon as you possibly can. Sincerely, Princess Celestia."

Twilight lowered the letter, and looked among her friends. She then said, "Well, I guess it's off to Trottingham then. Would you girls mind coming along?"

"Of course not, dear.", Rarity said, "I would never dream of letting a friend go off into a potentially dangerous situation."

"Yeah, what she said!", Pinkie Pie exclaimed, "Besides, it'll be a super fun mystery! Oh, I'd better go home and get my mystery solving hats!"

Before Pinkie could run off, Applejack was able to stop her, saying, "Er, ya know Pinkie, I really don't think that the hats'll be necessary. Last time you brought 'em out, we didn't know what the hay was goin' on at any point on that train ride."

Pinkie looked a little disappointed at this, but she kept her demeanor and said, "Well, okay. But when we get home, we're going to have the greatest 'We Solved the Big Trottingham Mystery Party' ever!"

"Won't it also be the only 'We Solved the Big Trottingham Mystery Party' ever?", Rainbow Dash pointed out.

"Exactly Dashie!", Pinkie Pie stated cheerfully, "Since it's the only 'We Solved the Big Trottingham Mystery Party', it automatically makes it the greatest 'We Solved the Big Trottingham Mystery Party' too!"

Rather than continuing to question Pinkie Pie about her line of reasoning, the others decided that it would probably be best to not think about it, as Pinkie Pie's logic wasn't exactly made to be thought through by anyone but the mare herself. So, in order to get to the task at hand, Twilight said, "Okay girls, we'd better get to Trottingham as soon as possible. And you can come if you want to Spike."

"Of course I'll come!", Spike said in an excited tone, "Writing that letter was the most excitement I've gotten all week."

"Alright then, let's go.", Twilight said, moving towards the doors leading out of the castle, her friends all following suit.

Later

The train ride was relatively short and uneventful, all things considered, but it was a good way for all of them to catch up after all that had happened for the past week. But still, the fact that a whole town had apparently went missing was still in the back of their brains. Yes, they were sure that they would beat whatever it was that came their way, yet they had absolutely no idea what they were in store for. Still, that didn't stop them from exiting the train when it entered the Trottingham station.

As the group walked onto the platform, they immediately noticed the silence. There was nothing but the sounds of the train, and a few ambient noises. And even then, they sounded pretty hollow too. It only took a few moments for Fluttershy to realize why, "I don't hear any animals..."

The others perked up their ears, and they all realized that she was right; there were no bird calls, no dogs barking, no frogs ribbiting, no... anything. Just the occasional breeze. It was almost surreal to experience complete silence like this, and it was making them all a little antsy. It was Rarity who broke the silence and said, "Oh, where is Princess Celestia? I know it's quite a distance from here to Canterlot, but still, I do hope she gets here soon. This place is giving me the creeps, and it can't be good for my complexion..."

"She probably just had to set up a lot of things is all.", Twilight explained, "Officially, when Princess Celestia leaves Canterlot, Princess Luna is the one who's in charge of things. So, she probably had to find Luna, tell her what was going on, tell the guards where she was going, and then come over here."

"And that's only if Luna's available too!", Spike added.

"Whew-we, bein' the ruler of Equestria must be hard if ya'll gotta go through all that stuff if ya wanna so much as leave the castle.", Applejack said.

"Well, that's just how it works I guess.", Twilight said, before white speck in the sky caught her eye. It took her a moment to realize what it was, but when she did, she smiled and said happily, "Well, it looks like we won't be waiting long, girls. Princess Celestia is on her way!"

The group turned toward where Twilight was looking, and indeed, they could see the white coat and flowing rainbow mane of Celestia, flying towards them. When she saw them, she dived down toward them, and gracefully landed in front of them. She then looked at them all in turn, and smiled warmly, saying, "Thank you all for coming. I'm glad that you're all willing to help with this matter."

"No trouble at all, your highness.", Rainbow said with a grin, before realizing, "Hey, wait a second, don't you usually come down here in a chariot or something like that?"

Celestia's face immediately became serious as she sighed and said, "Normally, yes, a pegasi pulled chariot would be how I'd get around. But this isn't a normal situation. I can't risk other ponies knowing about this until we know what's going on. They might start to panic, thinking that their town might be next. I wouldn't want them to find out only to lose their heads over nothing. I only want other ponies to know about everypony being missing if this is actually part of a much bigger problem. So, until then, I've been sure to keep quiet about it. And until we know for sure what's going on, I don't want any other ponies knowing. Can you all promise me that you'll keep this secret?"

Twilight nodded and said, "Of course, Princess. We promise."

"Good.", Celestia said, "Now, let's get to business. I think that we'll need to look around every inch of this place, and see if anyone is here. And if we can't find anyone, or reasonably determine what the cause of the disappearances were, we'll meet here in about an hour, and we'll all go to Canterlot to discuss this, agreed?"

The group nodded, and with that, they all split up to search the town.

Twilight immediately headed for town square, with Spike accompanying her. Indeed, the town looked as empty as the messenger had said, and everything looked to be untouched. After a few moments of wandering, Spike said, "Twilight, this place is really creeping me out... I mean where do you think everypony could've gone?"

"I have no idea, Spike.", Twilight answered, "But that's what we're here to find out. But I have no idea where to look..."

After mulling over the situation for a second, Spike realized something, "Hey, didn't you learn a magic detection spell waaaay back before we came to Ponyville?"

At first, Twilight was going to ask why Spike brought it up, but then she picked up on his train of thought and said, "Hey, you're right! If I use the spell, I can pick up residual magic in town, and figure out if magic was used to make all the ponies disappear! Spike, you're a genius!"

Spike smiled at the compliment as Twilight readied the spell, making her horn glow. As the spell started to take effect, her vision gained a purple tint, and words started to appear in the air, showing which spells were cast and where. As she looked all over, she could see the words _Levitation_ in fading letters, indicating that the most common unicorn spell wasn't used recently in Trottingham. After a few minutes, Spike asked, "You see anything Twilight."

"Nothing really out of the ordinary.", Twilight replied, "Just a lot of Levitation spells all over the place.", she then sighed and looked up, saying, "This isn't getting us anywhere. I-"

"Something wrong?", Spike asked.

"...Yeah... something's really wrong...", Twilight said, before flying up into the sky and taking a good look at the words that formed there.

Meanwhile, Fluttershy was roaming around the nearby forest, looking for any small animals, and much to her dismay, she couldn't find any. It was unsettling to be in complete silence like this, easpecially for a pony as jumpy as she was. It wasn't helped that usually when she came to places like this, the ambient sounds of nature were always there to calm her. But there wasn't even so much as a mouse squeaking. Sure, this place wasn't as bad as the Everfree Forest, but still, the thought of total isolation in the forest made her feel so small...

But then she heard a shuffle in the brush.

Fluttershy immediately went into panic mode and rushed to hide behind a tree, before peeking out a little to see what made the noise. She didn't see much of anything at first, but the shuffling continued. But after a few more moments, she saw what made the noise; a tiny robin, which looked just as scared as she was.

Instantly, Fluttershy's heart went out to the creature, and she came out from behind the tree saying, "Oh, you poor thing! I'm sorry, I didn't mean to be so frightened. I just didn't know what was making the noise and you can't be too careful."

The robin chirped sadly.

Fluttershy smiled as she held out her hoof so that the bird would jump onto it, which, after a few moments of hesitation, it did. She then said in an empathetic voice, "You're so small... you look like you can only barely fly... where are your momma and papa?"

The robin chirped sadly again.

"Oh, I see...", the yellow pegasus said, understanding the meanings behind the robin's small tweets. She then said, "Do you know what happened here?"

To anyone else, it sounded like the robin was just singing a nice, yet strangely sorrowful tune, like a regular bird. But to Fluttershy, it was a detailed account as to what had happened here much earlier. As soon as the robin finished, Fluttershy said, "Oh my... that's horrible! Thank goodness you were hiding in that bush when it happened."

The robin nodded.

"We have to tell Princess Celestia right away." Fluttershy said, making her way out of the forest.

Meanwhile, Applejack was searching around the outskirts, sort of between where the forest began and the town ended. Her strong hooves trotted at a steady pace as she scanned all over, looking for some sign of life, or at the very least a clue as to what had happened. She didn't find much of anything for quite some time, but she was determined, and kept on looking for something to find. And after about a half an hour of searching, she finally found something.

"Tracks...", she said to herself. These weren't like any other tracks in the dirt. These ones were pretty fresh by the looks of things. So, without much of anything else to do, she followed them, just to see where they went. She eventually came up to a house. The tracks went around the house, and Applejack followed, never once taking her eyes off of them. But then, after a few more moments of tracking, she came to a realization; she was right back in front of the house.

"What in tarnation is goin' on 'round here...?", she said to herself as she took another look at the tracks. At closer inspection, they appeared to be evenly spaced apart, and all four hooves were on the ground at the same time. Almost like the pony who left the tracks were... bouncing. But the only pony Applejack knew that bounced was-

"Hey Applejack!"

"Gah!", Applejack screamed, falling onto her back in a daze as Pinkie Pie giggled to herself. When Applejack regained her senses, she shouted, "Pinkie!? What the hay are you doin'!?

"Oh, I was looking for clues, like I was supposed to.", She explained, "And then I came to this house, and I looked all around it. Then, I found these tracks, and I decided to follow them to help lead me to who did this!"

Applejack sighed and said "Sorry, Sugercube. But you've been followin' yer own tracks for Celestia knows how long now."

"Aww, really?", Pinkie said, slightly disappointed, "Then I guess I made those tracks too, huh?", she continued, pointing her hoof at some tracks that led out from the door of the house and led to the outskirts from the opposite direction that Applejack came from.

Applejack immediately drew her attention to them and said, "Actually, Pinkie Pie... I think somepony else made 'em... c'mon let's follow 'em."

"Yay, I helped!", Pinkie exclaimed, following Applejack closely behind as they both followed the tracks. Applejack noted that they were faded, as though they were made a couple of days ago, but they were the freshest tracks, so they had to go somewhere. But then they abruptly stopped. And that's what really made Applejack scratch her head. There were now two more tracks, and a large amount of displaced dirt, like there was a struggle of some sort. She also noticed that the two tracks didn't seem to go anywhere. Like they just appeared out of nowhere. Already, a picture was forming in her head, and it wasn't a pretty one.

Up in the air, Rainbow Dash was flying around, looking for something on the ground that might help with the investigation. She looked all around her, taking note of Applejack and Pinkie Pie going down a road, Fluttershy coming out of the forest, and Twilight taking off into the air herself. So far, nothing that could be considered too far out of the ordinary. She sighed, and decided to take her eyes off the ground and look in the air. It was only a few short days ago she was here, attempting to help get Equestria's weather back on schedule again. Now everything was thrown out of whack again, and there was barely a cloud in the sky. Well, a cloud anyway.

At first Rainbow Dash thought nothing of the lonesome cloud in the middle of the sky, but after considering it a moment, she decided to take a look. After all, it was a very rare occurrence to see a single cloud on a clear day, even if the weather wasn't being controlled. Curious, she flew up to it to see what it was doing there. When she reached it, she looked at it carefully. It was a mid-sized cumulus cloud, which was strange, considering that since it was summer, the clouds were normally meant to be higher, and more importantly, not as small. She investigated it further, and much to her surprise, she found hoof prints, and rather large hoof prints at that. And the only pony Rainbow Dash knew who had hooves as big and as far apart as these was Princess Celestia. She raised her eyebrow, and spotted Celestia flying by a nearby clock tower. She sped over to the princess, and when she got there, Celestia looked at her and said, "Oh, hello Rainbow Dash. Did you find anything?"

"I'm not sure.", the rainbow-maned pegasus said, I found some hoof prints on a cloud, but they kinda look like yours."

Celestia raised her eyebrow and said, "But I didn't step on a cloud recently."

"Well, I don't know what to tell ya.", Rainbow replied, "They were all really big, and really far apart too."

Celestia closed her eyes in thought, and when she opened them, she said, "Alright. Show me the cloud."

As this was happening, Rarity was walking through various buildings, trying to look for anyone who might have been left behind. So far however, her search proved to be less than fruitful. Every building she came across was empty, and as the messenger said, everything was left untouched. And as Rarity went through more houses and businesses, the more she felt unsettled by the whole thing. Maybe this whole thing was indicative of a bigger problem...

Rarity shook her head. Now was not the time to panic. Not to mention that as far as she knew, this was an isolated incident, so it was entirely possible that this was a spell gone wrong, or some creature that could easily be dealt with.

As she tried to convince herself this, she had stepped on something that made a crackling noise. Curious, Rarity took a step back and looked at the ground, revealing that she had stood on a piece of paper. Rarity picked up the paper with her horn, and realized that it was a hastily scribbled note. It didn't take long for her to read the whole thing, and when she did, she immediately ran out of the house, and into the street, immediately turning her attention to the clock tower. Almost an hour had passed and she felt that it was about time she returned to the train station.

When she arrived, she was surprised to see that all the others had returned, and she was the last one to arrive. She took an open spot in the circle, and when she arrived, Celestia began to speak, "Alright, we've investigated the town for an hour. What have we found, my little ponies?"

Applejack was the first to step up, "Me an' Pinkie found what looked ta be a struggle near the outskirts of town. From what Ah could tell, two unicorns ganged up on somepony, and teleported him away."

"Yeah!", Pinkie blurted, "There were no tracks or anything! Just hooves that appeared out of nowhere, and then mysteeeeriously vanished, along with the first guy!"

Celestia nodded, "A good find. This proves that at least there might have been somepony who was left behind, before getting taken by something or somepony else."

Twilight then stepped forward, "Actually, I think the whole town was taken too. I did a magic detection spell, and up in the air, it said that a spell cast up there was something called, 'Mass Teleport'."

Celestia's ears perked, "Mass Teleport..."

"Yeah, and I think I know how it was up in the sky!", Rainbow said, "Me and Princess Celestia found some hoof prints in this cloud. He probably casted the spell from up there."

"But there wasn't a cloud from where I found the spell.", Twilight pointed out.

"It probably moved after a stiff breeze rolled it. A good enough wind from Ponyville could wind up here if a few pegasi got carried away.", Rainbow explained.

Celestia was silent for a moment, and then she said, "...Did anypony find anything else?"

Rarity stepped up and said, "I found this paper in one of the houses. There's a note on it, and it reads.", she cleared her throat and read, "'_Everypony outside is gone, and there are voices and bangs at the door. If anypony finds this, we are-_', and at that point, it just stops. Oh, the poor thing. They must have been scared senseless..."

"A-And it wasn't just the ponies who disappeared too.", Fluttershy said, holding out the robin, "Tim said that two big and mean ponies came into the forest, and teleported all the animals that they could find. He was the only one who got away because he was hiding."

Rainbow Dash raised her eyebrow, "You named it Tim?"

"He has his own name, but it's very hard to translate, so he said I could call him Tim...", Fluttershy replied meekly.

Princess Celestia's eyes were closed again, and she took a deep breath, as though she didn't want to believe what she was hearing. Eventually, she opened her eyes and said, "...Everypony, meet me in Canterlot. I need to look up some things. I'm sorry, but you'll have to go by train."

"It's alright Princess Celestia, we understand.", Twilight said.

Celestia nodded, and immediately took off for Canterlot, speeding away toward the castle. Whatever answers she might have had, it would have to wait until they all got there.


	3. A Hoof Is Pointed

Chapter Two- A Hoof is Pointed

Dust Cloud awoke in an awkward position. He was on his side, but his head was resting against something else, something cold. After blinking a few times in order to ward away the blurriness, he shakily stood up, and muttered an expletive due to his neck now being very sore. It took a few moments before he was able to gather his senses, but when he did, he wished that he hadn't, for the scene before him was something that he never expected to see, and he never wanted to see again; bars. There were bars everywhere, forming a cage around him. And not just him, but the hundreds of other ponies that crowded the room, which was just about as big as something that you would see in Canterlot Castle.

He backed up, away from the downtrodden faces and hopeless eyes, only to hit his flank against the bars that made up the back of the cage. His breathing became more heavy, and after a moment, he started to panic. What had happened to get him to this point? He was just a simple janitor, why would anyone want him in a place like this? Little did he know, but the answer was coming rather soon, in the form of a hulking beast trotting down the corridor of cages.

Dust Cloud could hear the creature before he saw it. The loud sound that it made while walking was more than enough to snap Dust Cloud of his temporary stupor and start to bare a new emotion; pure, unbridled fear. He pressed against the back of the cage, and soon, a large form stopped in front of him. He couldn't see what it was, but it was definitely pony in shape. He couldn't see it's face however, but it's voice more than made up for it. It was a deep baritone, and it's tone conveyed a sinister air. It chilled the poor little pony to the bone when it said, "Frightful, are we? Good. Your new master loves to see his slaves quake in his presence."

"S-Slave?", Dust asked, his fear making his voice quake.

"Oh yes.", the creature said, "We do enjoy seeing the lesser ponies know who the rightful ruler is. Now, if you would hold still..."

The cage opened, and the giant pony stepped in. A red glow appeared around a large horn, which converged toward the tip, and launched a beam at Dust's head. And in that moment, all he knew was sadness, despair, and sheer hopelessness...

"Now, if you would please step out of the cage, we can show you what you'll be doing for the rest of your days?", the giant pony said.

Dust said nothing in response, and with a despondent look, he hung his head and walked out of the cage, where a hooded unicorn waited for him. It lead him away from the area, and left the giant alone so that he could repeat the process on the next available pony...

Meanwhile

"Why couldn't we just fly here again?", Rainbow Dash asked, slightly annoyed.

The group was now just outside of Canterlot Castle, and were making their way to the throne room, where Princess Celestia awaited them. The group had taken the train to the city, and the long ride had made the many-colored pony more than a little antsy.

Twilight was the one who answered the pegasus' question, "Well, there are a few reasons. One, only three of us can fly, and two of us are not nearly as strong as you are. Two, we would be even weaker if we put the non-flying ponies on our backs. And three, Rarity is afraid of heights after the Best Young Fliers competition."

"Well, not heights, so much as flying...", Rarity said, slightly embarrassed after recalling the events of that day.

Rainbow Dash sighed and decided not to push the issue any further, instead now focusing her attention on the large door that led to the throne room at the end of the hall.

Inside...

"You're sure it's him, sister?", Luna asked, concern obvious in her voice.

Celestia nodded, "I am. No other pony has been able to perform feats of magic like this."

Luna said nothing, and sighed. She feared that this day would come, but she thought it never would. Oh, how wrong she was...

Celestia then continued, "It's alright, Luna. I already have the guards on high alert, and at least he can't steal our powers like Tirek."

"That still doesn't fill me with confidence...", Luna said.

After Luna spoke, a guard pony opened the door and said, "Princesses, The Princess of Friendship and her entourage have arrived. Shall I send them in?"

"Yes, of course.", Celestia said.

The guard pony nodded and opened the doors further, allowing the six ponies and one baby dragon inside the room. Wasting no time, Celestia and Luna flew over to them, and landed down on the ground in front of them. Celestia then said, "Hello again, my little ponies. I apologize for not bringing you here right away, but I wished to do some research of my own before coming to any conclusions."

Twilight's face betrayed a twinge of disappointment at not being able to help her mentor research for something, but she hid it well enough and said, "It's alright. We didn't mind taking the train."

Rainbow Dash was about to say something, but before she could, she was being jabbed in the side by Applejack, who said, "So, what exactly is it that happened?"

Celestia looked over to Luna, and they both nodded. Celestia then said, "Well... this is all very hard to explain... but suffice it to say... this all happened a long time ago."

"You mean like a thousand years ago?", Rainbow Dash asked."

Luna shook her head, "Not even close... this all happened since time immemorial..."

That got the pony's attention, even Pinkie Pie's. They all looked up at the princesses, as they began to spin their tale...

Celestia began, "If you've read a history book, then you'll know that the history of Equestria, and by extension, our entire world, starts with us taking the throne. But the history of the world goes back much further than that, for the world began with a very dark history."

"What do you mean?", Twilight asked.

"We have to start at the beginning.", Luna said, "The very beginning. A long time before my sister and I were even born, there was nothing. The sun and the moon moved erratically, and the world was nothing more than a sludge. But then... the first two ponies just... showed up."

"You mean you two?", Twilight asked.

Celestia shook her head, "No... our parents."

Jaws hit the floor. Spike spoke up, "Wait, you two had... parents!?"

They both nodded, and Celestia continued, "Yes. And out of the chaos that used to be our world, they forged our world. Father loved the sky, so with his magic, he created the clouds, weather, the stars, and put the sun and the moon under control. Mother loved nature, and created the plants and animals that inhabit our world. At first, they did their work separately, so they didn't know that they were crafting something beautiful together. But they eventually met, and fell in love. They didn't have names before they met, so they came up with names for each other. Mother was named Equinox, and father... he was named Eclipse.

"Together, they built a castle in the southern part of Equestria, and lived there peacefully for many years. Eventually, we were born, and our parents were overjoyed at this. They were growing bored with being all alone in the world that they created together, so having more ponies there made it a little more interesting. They doted on us, and they both loved us very much, and we loved them as well."

Luna smiled at a far off memory, "Father would entertain us by making the stars into various shapes, and mother would make statues and let us play with all the animals. And when we got bored with that, we would fly out all over the world, and see the things that they both created in those early days."

Celestia nodded and smiled warmly as well, "Yes, they were good days...", she then sighed, "But they wouldn't last forever, unfortunately. After many years of happiness, mother and Eclipse thought that more company could be used. So, they decided that they would create the many sentient creatures of this world. Eclipse tried his hoof at it first. He wanted a species that could be ruled over, and wouldn't mind being ruled over by him and his family, and in an effort to create this race, from the residual chaos left over in the world, he created the creatures who would later give birth to Discord and Tirek. After his frustration at their noncompliance and tricky natures, he took his raging emotions and turned them into the first griffons. However, they too weren't satisfactory creations to him, as they allowed their emotions to control them, rather than him. Getting frustrated, his rage created the first dragons, and we all know that they don't take orders well.

"After that, Eclipse gave up, and mother tried a different method. First, she drew on all her strength, and stomped down on the ground as hard as she could. From her hoof-print sprang the first earth ponies, who's strength and connection with the earth is legendary. Then, she plucked as many feathers as she could from her wings, and flung them into the air. From these, the first pegasi were made, and were able to soar with the birds and control the weather. And finally, with barely any strength left, she concentrated, and shot magic toward the ground, and from the crater, unicorns were made, and were able to use magic just as well as her. And because they were all born from her strength, body, and magic, they all were in her image, rather than the various forms that father's creations had taken on.

"Father was impressed at mother's creations, but he was also jealous. After all, she made all these wonderful things, but all of his creations were nothing more than destructive and uncooperative beings. But still, it didn't get to him at first. They established the land of Equestria, and all the ponies lived together in harmony. But after a few years, the power went to Eclipse's head... he soon wanted nothing less than the total subjugation of those under him. He began to issue policies that favored his more well liked race of ponies, the unicorns, and made the earth and pegasus ponies work harder. After this, animosity started to grow between the races. Mother tried to assuage some of their anger, but the damage was done. A civil war started.

"Eclipse attempted to stop it, but his methods were more than questionable. In secret, he created a spell that would make any pony he chose fall under his complete command. When he demonstrated it, mother was furious. Up until this point, she thought that Eclipse had only made a few mistakes in judgment, but after that... she knew that he couldn't be allowed to be in charge any more. So, with our help, we sealed him away..."

Both Luna and Celestia seemed to be saddened by this memory, but after a moment, Celestia continued, "We were both very young when this all happened... we barely understood what was happening at the time. All that mother told us was that he was doing bad things to the ponies that we all loved to play with, so she told us that we had to... seal him in Tartarus. We complied... but soon after it was done, we missed him... and so did mother. After it was over, mother fell into a depression, which lead to the long winter that eventually lead into the wendigo influx, which would lead into Hearth's Warming Eve, which would reunite the pony races under a common flag. A few years after that though, mother realized that she was no longer fit to rule, and passed leadership duties onto us... and that is where the history of Equestria officially starts."

The group stood in thought for a moment, letting the information dump that they received sink in. Twilight was the first to gather her thoughts, and said, "So... are you saying that your father..."

Celestia nodded, "Yes... it has taken him thousands of years... but he's back. King Eclipse has returned."

The ponies were awed. This was... nothing short of amazing. At first, they thought that this was nothing more than a simple mission to investigate a town that seemed to be missing it's population, fairly standard. But now... once again, the fate of Equestria was once again in the balance. But that didn't mean that the group didn't have questions, and Rainbow Dash was the first to voice hers, "So, wait a minute... why didn't you tell anypony about any of this? I mean, this kind of story sounds really important."

Luna was the one who answered, "We did not want anyone to remember father's treachery. It was a dark point in our history, and mother felt that it would be for the best that everything before that great civil war was just forgotten, including her after she left. There are a few remnants of his rule, however. For example, our crowns and necklaces were forged from father's own."

To the other ponies, this didn't sound too out of place, but to Rarity, this raised a question, "Well, hold on a moment... if you were able to melt his necklace and crown into those... then, how large was he?"

"He was practically triple our size when we were foals... and I'm sure that he's only grown further... at least double our current size.", Celestia answered.

The ponies and dragon looked wide-eyed. The more they heard about Eclipse, the less they wanted to meet him. However, they also knew that it was an inevitability, so they continued with questions, starting with Twilight asking, "So... where is your mother now?"

Celestia shook her head, "We don't know... the last time we saw her, she flew off into the sunset that I was creating. She said that she would return someday... but that day has yet to come..."

"Well, she doesn't sound like the best of mothers, if ya ask me.", Applejack said.

"Please understand,", Luna said, "Mother and father were wonderful parents once upon a time... but time has a way of making ponies hurt. So many years of isolation made father think that love was earned through subjection, and the years of seeing so many reminders of all the things that father did over the years made mother lose herself. However, she didn't just up and leave. She taught us how to control the sun and the moon, as well as politics."

"And speaking of that,", Pinkie Pie said, "Why did you leave in Hearth's Warming Eve if it was part of this super bad time? I mean, it makes for a great a party and all, but it can't be the only reason."

"It was the truest indication that Eclipse's power and influence was waning.", Celestia answered, "The pony races were starting to work together once again, and it showed that even the most vile of intentions become nothing after enough time has passed."

"Umm... can I ask something?", Fluttershy asked meekly.

"Of course.", Luna said, "What is it?"

"Umm... I found this robin back in Trottingham, and he said that it was two ponies that took his friends and family, and not a giant one... also, why would Eclipse even want animals?"

Celestia sighed, "I fear that Eclipse may have help... there are at least two other ponies who are following his command... they're either under his control, or they're doing it willingly... and I don't know which is worse. As for the animals... during the civil war, Eclipse used a spell to turn them feral, and would use them as infantry."

Fluttershy audibly gasped, beyond horrified. The mere thought of her little animal friends getting possessed by that vile pony... she couldn't let that happen to them! She held Tim the robin a little closer to her chest as reassurance, feeling a small level of comfort as the small bird flapped his wings and nuzzled into her fur.

"So, what'll it take to beat him?", Spike asked, "I mean, we already turned in the Elements of Harmony, and as far as we know, the Rainbow only worked once. So, what do we do?"

Celestia looked down, "As far as we know... we need the help of multiple alicorns in order to seal him away once again... but even then, we're not entirely sure it will work. It's why I went ahead of you all. I needed to research and see how much power would be needed to seal him away again. So far, results are... inconclusive."

"Well, what do you think we need?", Twilight asked.

"It took our mother, Luna and myself to seal him away.", Celestia answered, "But mother's magic was more powerful than either of ours, and neither of us can hope to reach her level. But since we have you and Cadence now, we were hoping that it would make things equal. Yet, we're still unsure about it... after all, Eclipse has likely grown in strength. Until we actually face him... we won't know how much power we'll need..."

"But we have allies, don't we?", Rarity asked, "The griffons hate him, and I'm sure that Discord would be more than willing to help make his day a little bit worse."

"We have already sent envoys to plead our case to the griffons, but they have a tendency to only care about things that would directly affect them.", Luna said, "And as for Discord... well, as soon as he caught wind of father's return, he came here and said something to the effect of, 'I'd rather be dead than face him head on.'. He then teleported away, and we've yet to hear from him again."

Applejack rolled her eyes, "Sounds like Discord alright... can't say Ah blame him though. He'd literally be meetin' his maker, and the maker wants him gone."

"He must be so frightened...", Fluttershy said quietly, "After all, if I knew that somepony would want to hurt me, I'd probably run away too..."

"He'll return eventually, I'm sure.", Celestia said, "But until he does, we can't count on him to do anything that will help our cause. But I can say for sure that he won't betray us again after what happened recently with Tirek. Yet I wish I knew for sure that he would help us..."

Twilight stepped closer to her mentor and said with confidence, "Well, whether he does or not, I promise you both that me and my friends will be able to help you fight against your father."

Shouts of affirmation came from the group, and a swell of confidence swept through them all. Even Fluttershy felt like she would be able to take on the world... well, a quarter of the world anyway.

Celestia and Luna smiled, and the elder sister said, "Thank you all...", her expression then turned to a more saddened one, "Unfortunately, I'm not sure what you would all be able to do to help us. Only Twilight has the power to help us stop Eclipse."

There was a moment of silence, as the group thought about how to help. Then, after a while, Rainbow Dash said, "Well, we could head to the different towns in Equestria, and act as lookouts. And if anything looks suspicious, then we'll stop it!"

"Yeah, I like that idea!", Pinkie Pie said, "And if that big meanie Eclipse shows up, then we'll warn you about it, and you can come over and take care of him!"

Celestia and Luna looked at each other for a moment, as though they were silently communicating about whether or not the plan had any merit. They were about to answer when the doors violently crashed open, revealing the haggard form of a pegasus pony guard. His wing looked bent out of shape and charred, as though it were hit by a bolt of magic. He stumbled down the hall before falling down on his side. Immediately, Celestia and Luna sprang into action, as well as the rest of the group when they realized what had just happened. The pony was panting horribly, and kept trying to form words, but they seemed to be coming out of his mouth silently. Celestia knelt down next to him and said in a calming tone, "Shhh... relax. Breathe slowly..."

The pegasus' breath slowed, and he grew calmer. Celestia then smiled down at him and said, "What's the matter?"

The pegasus took a deep breath, "I... I was going to Appleloosa... I was supposed to supervise trade between them and Canterlot merchants... th-then, out of nowhere, everyone was gone, and my wing was zapped by a pony wearing a hood... he said to come back here and tell you that... you are no longer in control... I-I don't know what it means, but..."

Luna bent down and said, "It's alright... you have done your duty, and you deserve a rest..."

Before the pegasus could say anything else, Luna's horn touched the pony's forehead, and he instantly fell into a deep and dreamless sleep. She then quickly turned toward another guard and ordered him to take him to the infirmary. The guard complied, and once more, the room was left in silence. Applejack was the first pony to break the silence, "Ah don't believe it... Appleloosa... gone..."

"It's just as we feared...", Celestia said, "Trottingham isn't the only town that Eclipse is planning on taking... and Appleloosa won't be the last. It's only a matter of time before he decides to take the citizens of another town, and we won't know which one will be next..."

"We need to make a plan, and fast.", Twilight said, "Who knows how many ponies Eclipse will take before we take action."

"Agreed.", Celestia said, "Also, until we're ready to take action, Luna and I would appreciate if you all would stay in Canterlot."

"We won't mind.", Twilight said.

"Good to hear.", Luna said, "But if you'll excuse me for a moment, I have to go and raise the moon. I'll be back soon."

Luna turned and stepped out onto a nearby balcony, but before she could even attempt to raise the moon, she looked up to see something that brought both fond memories, and great fear. She called out, "Sister! Hurry!"

At Luna's call, everyone who was inside the throne room ran out, and looked up to see what it was that Luna saw, and when they saw it, they all stood slack-jawed. In the middle of the sky, where the sun was meant to be, the moon was as well. The moon was covering the sun, and it left the world dark.

As soon as she saw it, Celestia tried to pull the sun away from the moon, and Luna joined in the effort attempting to move the moon away. Their efforts proved to be in vain, however, and the moon continued to block the sun.

"What... is that?", Spike asked.

"Father's specialty...", Luna said, sadness and anger welling inside her.


End file.
